TB-Profiler result

Run: SRR25827359
Summary

Run ID: SRR25827359

Sample name:

Date: 2024-04-15T11:04:10.505493

Number of reads: 18274242

Percentage reads mapped: 97.16

Median coverage: 483.0

Strain: lineage2.2.1;lineage3;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.2
lineage2 East-Asian RD105 0.36
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.36
lineage2.2 East-Asian (Beijing) RD105;RD207 0.34
lineage4 Euro-American None 0.44
lineage4.8 Euro-American (mainly T) RD219 0.39
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-12C>T Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Tyr141* Assoc w R
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
gyrA 7582 p.Asp94Gly missense_variant 0.53 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.98 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.33 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.44 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.25 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 0.82 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.26 pyrazinamide Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 0.16 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.12 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.28 ethambutol Assoc w R
ethA 4327051 p.Tyr141* stop_gained 0.18 ethionamide Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7374 p.Gln25Glu missense_variant 0.21 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7585 p.Ser95Thr missense_variant 0.54 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.57 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.19 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.54 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.28 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.32 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.57 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.37 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.21 rifampicin Not assoc w R
rpoB 762675 p.Leu957Val missense_variant 0.42 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 0.51 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.24 rifampicin Uncertain significance
rpoC 764918 p.Val517Leu missense_variant 0.21 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.54 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.31 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpR5 779274 p.Leu95Phe missense_variant 0.17 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 0.27 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781676 c.117C>T synonymous_variant 0.16 streptomycin Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.54 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.29 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.46 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.32 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 0.59 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.5 isoniazid Not assoc w R
katG 2154832 p.Leu427His missense_variant 0.2 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.57 pyrazinamide Not assoc w R
PPE35 2170048 p.Leu189Val missense_variant 0.15 pyrazinamide
PPE35 2170053 p.Thr187Ser missense_variant 0.13 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223491 c.-327C>A upstream_gene_variant 0.42 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289365 c.-125delC upstream_gene_variant 0.24 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.23 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.21 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
thyA 3074529 c.-58G>C upstream_gene_variant 0.16 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.59 cycloserine
whiB7 3568889 c.-211_-210insG upstream_gene_variant 0.2 streptomycin Uncertain significance
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.39 pyrazinamide Not assoc w R - Interim
lpqB 3624756 p.Leu52Ser missense_variant 0.16 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.54 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625418 p.Leu399Arg missense_variant 0.17 bedaquiline
rifampicin
mtrB 3626125 c.489C>A synonymous_variant 0.4 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.37 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841590 c.-170G>A upstream_gene_variant 0.17 cycloserine
alr 3841609 c.-190_-189insAAGC upstream_gene_variant 0.29 cycloserine
panD 4044872 c.-591C>T upstream_gene_variant 0.21 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.22 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.26 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.17 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.35 ethambutol Not assoc w R
embB 4246544 p.Thr11Pro missense_variant 0.27 ethambutol Uncertain significance
embB 4246548 p.Pro12Gln missense_variant 0.27 ethambutol Uncertain significance
embB 4246555 c.42G>C synonymous_variant 0.23 ethambutol
embB 4246556 p.Ala15Pro missense_variant 0.23 ethambutol Uncertain significance
embB 4246563 p.Leu17Trp missense_variant 0.27 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.22 ethambutol Not assoc w R - Interim
embB 4246811 p.Gly100Ser missense_variant 0.38 ethambutol Uncertain significance
embB 4247028 p.Leu172Arg missense_variant 0.2 ethambutol
embB 4247039 p.Phe176Val missense_variant 0.15 ethambutol
aftB 4267088 c.1749C>T synonymous_variant 0.18 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.39 ethambutol Not assoc w R
aftB 4268753 c.84T>G synonymous_variant 0.16 ethambutol Not assoc w R - Interim
ethA 4326963 p.Leu171Phe missense_variant 0.17 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.52 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.55 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.23 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.3 streptomycin Not assoc w R